Inhibition of histone deacetylase as a treatment for cardiac hypertrophy

ABSTRACT

The present invention provides for methods of treating and preventing cardiac hypertrophy. Class II HDACs, which are known to participate in regulation of chromatin structure and gene expression, have been shown to have beneficial effects on cardiac hypertrophy. Surprisingly, the present invention demonstrates that HDAC inhibitors inhibit cardiac hypertrophy by inhibiting fetal cardiac gene expression and interfering with sarcomeric organization.

The present invention claims benefit of priority to and is acontinuation of U.S. Ser. No. 10/256,221, filed Sep. 26, 2002, nowissued as U.S. Pat. No. 6,706,686, which claims priority to U.S.Provisional Ser. Nos. 60/325,311, filed Sep. 27, 2001, and 60/334/041,filed Oct. 31, 2001, the entire contents of which are herebyincorporated by reference without reservation.

The government owns rights in the present invention pursuant to grantnumber NIH RO1 HL61544 from the National Institutes of Health.

BACKGROUND OF THE INVENTION

1. Field of the Invention

The present invention relates generally to the fields of developmentalbiology and molecular biology. More particularly, it concerns generegulation and cellular physiology in cardiomyocytes. Specifically, theinvention relates to the use of HDAC inhibitors to treat cardiachypertrophy and heart failure.

2. Description of Related Art

Cardiac hypertrophy in response to an increased workload imposed on theheart is a fundamental adaptive mechanism. It is a specialized processreflecting a quantitative increase in cell size and mass (rather thancell number) as the result of any or a combination of neural, endocrineor mechanical stimuli. Hypertension, another factor involved in cardiachypertrophy, is a frequent precursor of congestive heart failure. Whenheart failure occurs, the left ventricle usually is hypertrophied anddilated and indices of systolic function, such as ejection fraction, arereduced. Clearly, the cardiac hypertrophic response is a complexsyndrome and the elucidation of the pathways leading to cardiachypertrophy will be beneficial in the treatment of heart diseaseresulting from a various stimuli.

A family of transcription factors, the myocyte enhancer factor-2 family(MEF2), are involved in cardiac hypertrophy. For example, a variety ofstimuli can elevate intracellular calcium, resulting in a cascade ofintracellular signaling systems or pathways, including calcineurin, CAMkinases, PKC and MAP kinases. All of these signals activate MEF2 andresult in cardiac hypertrophy. However, it is still not completelyunderstood how the various signal systems exert their effects on MEF2and modulate its hypertrophic signaling. It is known that certainhistone deacetylase proteins, HDAC 4, HDAC 5, HDAC 7, HDAC 9, and HDAC10, are involved in modulating MEF2 activity.

Eleven different HDACs have been cloned from vertebrate organisms. Allshare homology in the catalytic region. Histone acetylases anddeacetylases play a major role in the control of gene expression. Thebalance between activities of histone acetylases, usually called acetyltransferases (HATs), and deacetylases (HDACS) determines the level ofhistone acetylation. Consequently, acetylated histones cause relaxationof chromatin and activation of gene transcription, whereas deacetylatedchromatin is generally transcriptionally inactive. In a previous report,the inventors' laboratory demonstrated that HDAC 4 and 5 dimerize withMEF2 and repress the transcriptional activity of MEF2 and, further, thatthis interaction requires the presence of the N-terminus of the HDAC 4and 5 proteins. McKinsey et al. (2000a,b).

In a distinct context, recent research has also highlighted theimportant role of HDACs in cancer biology. In fact, various inhibitorsof HDACs are being tested for their ability to induce cellulardifferentiation and/or apoptosis in cancer cells. Marks et al. (2000).Such inhibitors include suberoylanilide hydroxamic acid (SAHA) (Butleret al., 2000; Marks et al., 2001); m-carboxycinnamic acidbis-hydroxamide (Coffey et al., 2001); and pyroxamide (Butler et al.,2001). These studies have been summarized as indicating “that thehydroxamic acid-based HPCs, in particular SAHA and pyroxamide—are potentinhibitors of HDAC in vitro and in vivo and induce growth arrest,differentiation, or apoptotic cell death of transformed cells . . . [andthus] are lead compounds among the family of hydroxamic acid-based HPCsand are currently in phase I clinical trials.” Marks et al. (2000). Todate, no reports on the effects of HDAC inhibitors on muscle cellhypertrophy and response to stress have been reported.

SUMMARY OF THE INVENTION

Thus, in accordance with the present invention, there is provided amethod of treating pathologic cardiac hypertrophy and heart failurecomprising (a) identifying a patient having cardiac hypertrophy; and (b)administering to the patient a histone deacetylase inhibitor.Administering may comprise intravenous, oral, transdermal, sustainedrelease, suppository, or sublingual administration. The method mayfurther comprise administering a second therapeutic regimen, such as abeta blocker, an iontrope, diuretic, ACE-I, AII antagonist orCa⁺⁺-blocker. The second therapeutic regimen may be administered at thesame time as the histone deacetylase inhibitor, or either before orafter the histone deacetylase inhibitor. The treatment may improve oneor more symptoms of cardiac failure such as providing increased exercisecapacity, increased blood ejection volume, left ventricular enddiastolic pressure, pulmonary capillary wedge pressure, cardiac output,cardiac index, pulmonary artery pressures, left ventricular end systolicand diastolic dimensions, left and right ventricular wall stress, walltension and wall thickness, quality of life, disease-related morbidityand mortality.

In yet another embodiment, there is provided a method of preventingpathologic cardiac hypertrophy and heart failure comprising (a)identifying a patient at risk of developing cardiac hypertrophy; and (b)administering to the patient a histone deacetylase inhibitor.Administration may comprise intravenous, oral, transdermal, sustainedrelease, suppository, or sublingual administration. The patient at riskmay exhibit one or more of long standing uncontrolled hypertension,uncorrected valvular disease, chronic angina and/or recent myocardialinfarction.

In accordance with the preceding embodiments, the histone deacetylaseinhibitor may be any molecule that effects a reduction in the activityof a histone deacetylase. This includes proteins, peptides, DNAmolecules (including antisense), RNA molecules (including RNAi andantisense) and small molecules. The small molecules include, but are notlimited to, trichostatin A, trapoxin B, MS 275-27, m-carboxycinnamicacid bis-hydroxamide, depudecin, oxamflatin, apicidin, suberoylanilidehydroxamic acid, Scriptaid, pyroxamide,2-amino-8-oxo-9,10-epoxy-decanoyl,3-(4-aroyl-1H-pyrrol-2-yl)-N-hydroxy-2-propenamide and FR901228.Additionally, the following references describe histone deacetylaseinhibitors which may be selected for use in the current invention: AU9,013,101; AU 9,013,201; AU 9,013,401; AU 6,794,700; EP 1,233,958; EP1,208,086; EP 1,174,438; EP 1,173,562; EP 1,170,008; EP 1,123,111; JP2001/348340; U.S. 2002/103192; U.S. 2002/65282; U.S. 2002/61860; WO02/51842; WO 02/50285; WO 02/46144; WO 02/46129; WO 02/30879; WO02/26703; WO 02/26696; WO 01/70675; WO 01/42437; WO 01/38322; WO01/18045; WO 01/14581; Furumai et al. (2002); Hinnebusch et al. (2002);Mai et al. (2002); Vigushin et al. (2002); Gottlicher et al. (2001);Jung (2001); Komatsu et al. (2001); Su et al. (2000).

In still another embodiment, there is provided a method of identifyinginhibitors of cardiac hypertrophy comprising (a) providing a histonedeacetylase inhibitor; (b) treating a myocyte with the histonedeacetylase inhibitor; and (c) measuring the expression of one or morecardiac hypertrophy parameters, wherein a change in the one or morecardiac hypertrophy parameters, as compared to one or more cardiachypertrophy parameters in a myocyte not treated with the histonedeacetylase inhibitor, identifies the histone deacetylase inhibitor asan inhibitor of cardiac hypertrophy. The myocyte may be subjected to astimulus that triggers a hypertrophic response in the one or morecardiac hypertrophy parameters, such as expression of a transgene ortreatment with a drug.

The one or more cardiac hypertrophy parameters may comprise theexpression level of one or more target genes in the myocyte, wherein theexpression level of the one or more target genes is indicative ofcardiac hypertrophy. The one or more target genes may be selected fromthe group consisting of ANF, α-MyHC, β-MyHC, α-skeletal actin, SERCA,cytochrome oxidase subunit VIII, mouse T-complex protein, insulin growthfactor binding protein, Tau-microtubule-associated protein, ubiquitincarboxyl-terminal hydrolase, Thy-1 cell-surface glycoprotein, or MyHCclass I antigen. The expression level may be measured using a reporterprotein coding region operably linked to a target gene promoter, such asluciferase, β-gal or green fluorescent protein. The expression level maybe measured using hybridization of a nucleic acid probe to a target mRNAor amplified nucleic acid product.

The one or more cardiac hypertrophy parameters also may comprise one ormore aspects of cellular morphology, such as sarcomere assembly, cellsize, or cell contractility. The myocyte may be an isolated myocyte, orcomprised in isolated intact tissue. The myocyte also may be acardiomyocyte, and may be located in vivo in a functioning intact heartmuscle, such as functioning intact heart muscle that is subjected to astimulus that triggers a hypertrophic response in one or more cardiachypertrophy parameters. The stimulus may be aortic banding, rapidcardiac pacing, induced myocardial infarction, or transgene expression.The one or more cardiac hypertrophy parameters comprises right ventricleejection fraction, left ventricle ejection fraction, ventricular wallthickness, heart weight/body weight ratio, or cardiac weightnormalization measurement. The one or more cardiac hypertrophyparameters also may comprise total protein synthesis.

In still yet another embodiment, there is provided a method ofidentifying inhibitors of cardiac hypertrophy comprising (a) providingat least one class I and one class II histone deacetylase; (b)contacting the histone deacetylases with a candidate inhibitorsubstance; and (c) measuring the activity of the histone deacetylases,wherein a greater decrease in class I histone deacetylase activity thanclass II histone deacetylase activity identifies the candidate inhibitorsubstance as an inhibitor of cardiac hypertrophy. The histonedeacetylases may be purified away from whole cells or located in anintact cell. The cell may be a myocyte, such as a cardiomyocyte.Measuring HDAC activity may comprise measuring release of a labeledacetyl group from a histone. The label may be a radiolabel, afluorescent label or a chromophore.

The class I histone deacetylase may be HDAC1, HDAC2, HDAC3, or HDAC 8.The class II histone deacetylase may be HDAC4, HDAC5, HDAC6, HDAC7,HDAC9, or HDAC 10. The activity of more than one class I histonedeacetylase may be measured. The activity of more than one class IIhistone deacetylase may be measured. The activity of more than one classI histone deacetylase and more than one class II histone deacetylase maybe measured. The candidate inhibitor substance may have inhibitoryactivity against at least one class I histone deacetylase and have noactivity against at least one class II histone deacetylase. Thecandidate inhibitor substance may have inhibitory activity againstmultiple class I histone deacetylases and have no activity againstmultiple class II histone deacetylases. The candidate inhibitorsubstance may have inhibitory activity against at least one class Ihistone deacetylase that is at least two-fold greater than itsinhibitory activity against at least one class II histone deacetylase.The candidate inhibitor substance may have inhibitory activity againstat least one class I histone deacetylase that is at least five-foldgreater than its inhibitory activity against at least one class IIhistone deacetylase.

BRIEF DESCRIPTION OF THE DRAWINGS

The following drawings form part of the present specification and areincluded to further demonstrate certain aspects of the presentinvention. The invention may be better understood by reference to one ormore of these drawings in combination with the detailed description ofspecific embodiments presented herein.

FIGS. 1A-C. TSA alters agonist-induced gene repression. Cultured cardiacmyocytes were treated with PE (20 μmol/L) or IL-1 (1 ng/mL) for 48 hrs.TSA (30 nmol/L) was added 30 min. prior to treatment with PE or IL-1.Myocyte-specific mRNA expression (SERCA2a (FIG. 1A), αMyHC (FIG. 1B),βMyHC (FIG. 1C) was assayed in 5 μg total RNA by RNase protection assay.Mean data are from 4 cultures, and are presented as % of control afternormalization to GAPDH signal.

FIGS. 2A-D. Over-expression of HDACs repress muscle-specific promoters.Cultured myocytes were transfected for 72 hrs. with expression vectors(2 μg per ˜3×105 cells) for Flag-tagged HDAC1, 4, 5 (or its backbonevector) and CAT reporter (5 μg) constructs for SERCA (FIG. 2A), αMyHC(FIG. 2B), βMyHC (FIGS. 2C and 2D) genes, plus SV40-driven secretedalkaline phosphatase (SEAP 1 μg, Clontech). TSA was used at 30 nmol/L,and added just after the transfection. PE 22 (20 μmol/L) was added 24hrs. later and CAT assays performed after an additional 48 hours. Meandata are from n=3 different cultures, and are presented as % of pCMVafter normalization to SEAP activity in the media. Over-expression ofHDAC was confirmed by Western blot for Flag.

FIGS. 3A-D. HDAC inhibitors block the activation of ANF reporter byphenylphrine without cytotoxicity. Neonatal rat cardiomyocytes wereco-transfected with a total of 1 μg of the mouse 3 kb ANF promoterfragment and CMV-Lac Z plasmids. (FIG. 3A) The ANF promoter is minimallyactive in unstimulated cardiomyocytes. The addition of HDAC inhibitorsdoes not induce ANF promoter activity. Addition of phenylphrineactivated the ANF promoter, but co-treatment of cardiomyoyctes withphenylephrine and a HDAC inhibitor (TSA (85 nM), NaBut (5 mM), orHC-toxin (5 ng/ml)) prevented the activation of the ANF promoter byphenylphrine (100 μM). (FIG. 3B) Lac Z expression by the constitutivepromoter CMV. Treatment with HDAC inhibitors augmented CMV activity withand without phenylephrine co-treatment. (FIGS. 3C and 3D) The graphsshow the measurements of adenylate kinase activity remains constant inthe medium after X hours of culturing cardiomyocytes in the absence orpresence of hypertrophic stimulants FBS, PE or ET-1.

FIGS. 4A-C. HDAC inhibitors prevent endogenous ANF expression normallyinduced by hypertrophic agonists. (FIG. 4A) Graph shows the summation ofseveral dot blot experiments (n=4). As in the transfection experiments,phenylephrine (100 □M) induces ANF expression over three-fold. Treatmentwith HDAC inhibitors (TSA 85 nM; sodium butyrate, 5 mM; HC-toxin 5ng.ml) blocks the accumulation of ANF message. (FIGS. 4B and 4C) Thegraphs show a reduction of the chemiluminent detection of ANF in theculture medium with increasing concentrations of the HDAC inhibitors TSA(FIG. 4B) and sodium butyrate (FIG. 4C) when co-cultured with thehypertrophic stimulants FBS, PE or ET-1.

FIGS. 5A-B. Treatment of cardiomyocytes with HDAC inhibitors blocks thefetal gene program associated with cardiomyocyte hypertrophy. (FIG. 5A)Graph shows fold changes in αSK-actin expression by phenylephrine andthe lack of gene activation in TSA-treated samples. (FIG. 5B) Graphshows the fold changes of αMyHC and βMyHC RNA expression. Phenylephrinetreatment induces the activation of βMyHC expression (fetal gene) incardiomyocytes; whereas, phenylephrine alone does not active the αMyHCgene, the adult isoform. Treatment with TSA prevented the activation ofβMyHC but stimulated the expression of αMyHC. The graphs represent threeor more independent experiments

FIG. 6. The effects of TSA treatment on the reorganization of thesarcomeres and protein synthesis. Graphs of the measurements of S6ribosome protein in cardiomyocytes shows that phenylephrine and serumincreases protein synthesis in cardiomyocytes. Treatment ofcardiomyocytes with TSA does not alter this increase after 6 hours(graphs on left). The graphs on the right show the content of S6ribosome protein in cardiomyocytes after 24 hours co-treatment with PEand increasing concentrations of TSA or with serum and increasingconcentrations of TSA.

FIGS. 7A-B. TSA induces the activation of genes that are involved incardiomyocyte differentiation. (FIG. 7A) Three genes were up-regulatedby phenylephrine and down-regulated by TSA. (FIG. 7B) Four genes wereinactivated by phenylephrine and activated by TSA (results from onephenylephrine chip, two phenylephrine/TSA chips, and one TSA chip.)

DESCRIPTION OF ILLUSTRATIVE EMBODIMENTS

Heart failure is one of the leading causes of morbidity and mortality inthe world. In the U.S. alone, estimates, indicate that 3 million peopleare currently living with cardiomyopathy and another 400,000 arediagnosed on a yearly basis. Dilated cardiomyopathy (DCM), also referredto as “congestive cardiomyopathy,” is the most common form of thecardiomyopathies and has an estimated prevalence of nearly 40 per100,000 individuals (Durand et al., 1995). Although there are othercauses of DCM, familiar dilated cardiomyopathy has been indicated asrepresenting approximately 20% of “idiopathic” DCM. Approximately halfof the DCM cases are idiopathic, with the remainder being associatedwith known disease processes. For example, serious myocardial damage canresult from certain drugs used in cancer chemotherapy (e.g., doxorubicinand daunoribucin). In addition, many DCM patients are chronicalcoholics. Fortunately, for these patients, the progression ofmyocardial dysfunction may be stopped or reversed if alcohol consumptionis reduced or stopped early in the course of disease. Peripartumcardiomyopathy is another idiopathic form of DCM, as is diseaseassociated with infectious sequelae. In sum, cardiomyopathies, includingDCM, are significant public health problems.

As cardiomyopathy itself typically does not produce any symptoms untilthe cardiac damage is severe enough to produce heart failure, thesymptoms of cardiomyopathy are those associated with heart failure.These symptoms include shortness of breath, fatigue with exertion, theinability to lie flat without becoming short of breath (orthopnea),paroxysmal nocturnal dyspnea, enlarged cardiac dimensions, and/orswelling in the lower legs. Patients also often present with increasedblood pressure, extra heart sounds, cardiac murmurs, pulmonary andsystemic emboli, chest pain, pulmonary congestion, and palpitations. Inaddition, DCM causes decreased ejection fractions (i.e., a measure ofboth intrinsic systolic function and remodeling). The disease is furthercharacterized by ventricular dilation and grossly impaired systolicfunction due to diminished myocardial contractility, which results indilated heart failure in many patients. Affected hearts also undergocell/chamber remodeling as a result of the myocyte/myocardialdysfunction, which contributes to the “DCM phenotype.” As the diseaseprogresses, the symptoms progress as well. Patients with dilatedcardiomyopathy also have a greatly increased incidence oflife-threatening arrhythmias, including ventricular tachycardia andventricular fibrillation. In these patients, an episode of syncope(dizziness) is regarded as a harbinger of sudden death.

Diagnosis of dilated cardiomyopathy typically depends upon thedemonstration of enlarged heart chambers, particularly enlargedventricles. Enlargement is commonly observable on chest X-rays, but ismore accurately assessed using echocardiograms. DCM is often difficultto distinguish from acute myocarditis, valvular heart disease, coronaryartery disease, and hypertensive heart disease. Once the diagnosis ofdilated cardiomyopathy is made, every effort is made to identify andtreat potentially reversible causes and prevent further heart damage.For example, coronary artery disease and valvular heart disease must beruled out. Anemia, abnormal tachycardias, nutritional deficiencies,alcoholism, thyroid disease and/or other problems need to be addressedand controlled.

During attempts to identify and stabilize the underlying cause of thecardiomyopathy, treatment is generally instituted in order to minimizethe symptoms and optimize the efficiency of the failing heart.Medication remains the mainstay of treatment, although there are nospecific treatments for dilated cardiomyopathy other than those used inheart failure cases in general. Transplant surgery is one option.Indeed, dilated cardiomyopathy has been indicated as the most commoncause for cardiac transplantation in the U.S.

Non-pharmacological treatment is primarily used as an adjunct topharmacological treatment. One means of non-pharmacological treatmentinvolves reducing the sodium in the diet. In addition,non-pharmacological treatment also entails the elimination of certainprecipitating drugs, including negative inotropic agents (e.g., certaincalcium channel blockers and antiarrhythmic drugs like disopyramide),cardiotoxins (e.g., amphetamines), and plasma volume expanders (e.g.,nonsteroidal anti-inflammatory agents and glucocorticoids).

Treatment with pharmacological agents represents the primary mechanismfor reducing or eliminating the manifestations of heart failure.Diuretics constitute the first line of treatment for mild-to-moderateheart failure. Unfortunately, many of the commonly used diuretics (e.g.,the thiazides) have numerous adverse effects. For example, certaindiuretics may increase serum cholesterol and triglycerides. Moreover,diuretics are generally ineffective for patients suffering from severeheart failure.

If diuretics are ineffective, vasodilatory agents may be used; theangiotensin converting (ACE) inhibitors (e.g., enalopril and lisinopril)not only provide symptomatic relief, they also have been reported todecrease mortality (Young et al., 1989). Again, however, the ACEinhibitors are associated with adverse effects that result in theirbeing contraindicated in patients with certain disease states (e.g.,renal artery stenosis).

Similarly, inotropic agent therapy (i.e., a drug that improves cardiacoutput by increasing the force of myocardial muscle contraction) mayalso be indicated if the diuretics do not result in adequate relief. Theinotropic agent most commonly used by ambulatory patients is digitalis.However, it is associated with a panoply of adverse reactions, includinggastrointestinal problems and central nervous system dysfunction.

Thus, the currently used pharmacological agents have severe shortcomingsin particular patient populations. The availability of new, safe andeffective agents would undoubtedly benefit patients who either cannotuse the pharmacological modalities presently available, or who do notreceive adequate relief from those modalities. The prognosis forpatients with DCM is variable, and depends upon the degree ofventricular dysfunction, with the majority of deaths occurring withinfive years of diagnosis.

I. The Present Invention

The inventors have shown previously that MEF2 is activated by MAP kinasephosphorylation of three conserved sites in its carboxy-terminalactivation domain (see, Katoh et al 1998). CaMK signaling also activatesMEF2 by phosphorylating the class II HDACs, which are expressed at highlevels in the adult heart where they can repress MEF2 activity. Uponphosphorylation, these HDACs bind to 14-3-3, and dissociate from MEF2,with resulting translocation to the nucleus and activation ofMEF2-dependent transcription. Mutants of class II HDACs that cannot bephosphorylated cannot detach from MEF2 and irreversibly block expressionof MEF2 target genes.

It has also been shown that an adenovirus encoding anon-phosphorylatable mutant of HDAC 5 is capable of preventingcardiomyocyte hypertrophy in vitro in response to diverse signalingpathways (see, Lu et al., 2000). These findings suggest thatphosphorylation of these conserved sites in class II HDACs is anessential step for initiating cardiac hypertrophy. Based on thesefinding, one might expect that inhibition of HDAC activity by TSA wouldresult in the induction of cardiac hypertrophy because of derepressionof hypertrophic responsive genes. On the contrary, the present inventorsfound instead that TSA actually prevents cardiac hypertrophy. Theseunexpected findings suggest that at least some HDACs are required forhypertrophy and that inhibition of HDAC catalytic activity can preventactivation of hypertrophic genes.

How can these apparently conflicting results be explained? One modelargues that class I and II HDACs may control different sets of genes incardiomyocytes. According to this model, class II HDACs interact withand repress the activity of transcription factors, such as MEF2, thatare required for hypertrophy, which would explain whynon-phosphorylatable mutants of class II HDACs block hypertrophy. Incontrast, it is proposed that class I HDACs, HDAC 1 and HDAC 3 inparticular, suppress the expression of anti-hypertrophic genes. Thus,exposure of cardiomyocytes to TSA would result in derepression of theseanti-hypertrophic genes and a blockade of hypertrophy. This model alsopredicts that the activity of such anti-hypertrophic genes would bedominant over the activity of class II HDACs, since they too arerepressed by TSA, which would be expected to derepress the hypertrophicprogram.

In any event, and regardless of the precise molecular basis, the presentinvention shows that, surprisingly, HDAC inhibitors are beneficial inthe treatment of cardiac hypertrophy and heart failure.

II. Histone Deacetylase

Nucleosomes, the primary scaffold of chromatin folding, are dynamicmacromolecular structures, influencing chromatin solution conformations(Workman and Kingston, 1998). The nucleosome core is made up of histoneproteins, H2A, HB, H3 and H4. Histone acetylation causes nucleosomes andnucleosomal arrangements to behave with altered biophysical properties.The balance between activities of histone acetyl transferases (HAT) anddeacetylases (HDAC) determines the level of histone acetylation.Acetylated histones cause relaxation of chromatin and activation of genetranscription, whereas deacetylated chromatin generally istranscriptionally inactive.

Eleven different HDACs have been cloned from vertebrate organisms. Thefirst three human HDACs identified were HDAC 1, HDAC 2 and HDAC 3(termed class I human HDACs), and HDAC 8 (Van den Wyngaert et al., 2000)has been added to this list. Recently class II human HDACs, HDAC 4, HDAC5, HDAC 6, HDAC 7, HDAC 9, and HDAC 10 (Kao et al., 2000) have beencloned and identified (Grozinger et al., 1999; Zhou et al. 2001; Tong etal., 2002). Additionally, HDAC 11 has been identified but not yetclassified as either class I or class II (Gao et al., 2002). All sharehomology in the catalytic region. HDACs 4, 5, 7, 9 and 10 however, havea unique amino-terminal extension not found in other HDACs. Thisamino-terminal region contains the MEF2-binding domain. HDACs 4, 5 and 7have been shown to be involved in the regulation of cardiac geneexpression and in particular embodiments, repressing MEF2transcriptional activity. The exact mechanism in which class II HDAC'srepress MEF2 activity is not completely understood. One possibility isthat HDAC binding to MEF2 inhibits MEF2 transcriptional activity, eithercompetitively or by destabilizing the native, transcriptionally activeMEF2 conformation. It also is possible that class II HDAC's requiredimerization with MEF2 to localize or position HDAC in a proximity tohistones for deacetylation to proceed.

III. Deacetylase Inhibitors

A variety of inhibitors for histone deacetylase have been identified.The proposed uses range widely, but primarily focus on cancer therapy.Saunders et al. (1999); Jung et al. (1997); Jung et al. (1999); Vigushinet al. (1999); Kim et al. (1999); Kitazomo et al. (2001); Vigusin et al.(2001); Hoffmann et al. (2001); Kramer et al. (2001); Massa et al.(2001); Komatsu et al. (2001); Han et al. (2001). Such therapy is thesubject of an NIH sponsored Phase I clinical trial for solid tumors andnon-Hodgkin's lymphoma. HDAC's also increase transcription oftransgenes, thus constituting a possible adjunct to gene therapy. Yamanoet al. (2000); Su et al. (2000).

HDACs can be inhibited through a variety of differentmechanisms—proteins, peptides, and nucleic acids (including antisenseand RNAi molecules). Methods are widely known to those of skill in theart for the cloning, transfer and expression of genetic constructs,which include viral and non-viral vectors, and liposomes. Viral vectorsinclude adenovirus, adeno-associated virus, retrovirus, vaccina virusand herpesvirus.

Also contemplated are small molecule inhibitors. Perhaps the most widelyknown small molecule inhibitor of HDAC function is Trichostatin A, ahydroxamic acid. It has been shown to induce hyperacetylation and causereversion of ras transformed cells to normal morphology (Taunton et al.,1996) and induces immunsuppression in a mouse model (Takahashi et al.,1996). It is commercially available from BIOMOL Research Labs, Inc.,Plymouth Meeting, Pa.

The following references, incorporated herein by reference, all describeHDAC inhibitors that may find use in the present invention: AU9,013,101; AU 9,013,201; AU 9,013,401; AU 6,794,700; EP 1,233,958; EP1,208,086; EP 1,174,438; EP 1,173,562; EP 1,170,008; EP 1,123,111; JP2001/348340; U.S. 2002/103192; U.S. 2002/65282; U.S. 2002/61860; WO02/51842; WO 02/50285; WO 02/46144; WO 02/46129; WO 02/30879; WO02/26703; WO 02/26696; WO 01/70675; WO 01/42437;WO 01/38322; WO01/18045; WO 01/14581; Furumai et al. (2002); Hinnebusch et al. (2002);Mai et al. (2002); Vigushin et al. (2002); Gottlicher et al. (2001);Jung (2001); Komatsu et al. (2001); Su et al. (2000).

Examples of some specific HDAC inhibitors are shown in Table 1.

TABLE 1 Chemical Inhibitor Compound Type Composition Organism Trapoxin Bporphyrin derivative C₃₃H₃₀N₄O₆ H. ambiens MS-27-275 benzamideC₂₁H₂₀N₄O3 derivative Scriptaid hydroxamic acid C₁₈H₁₂N₂O₄ FR901228cyclopeptide C₂₄H₃₆N₄O₆S₂ C. violaceum (#968) Depudecin fungalmetabolite C₁₁H₁₆O₄ A. brassiciola Oxamflatin aromatic C₁₈H₁₄N₂O₄S₁sulfonamide Pyroxamide hydroxamic acid C₁₃H₂₀N₃O₃ (suberoyl-3-aminopyridineamide hydroxyamic acid) 2-amino-8-oxo- ketone C₁₀H₁₇NO₃9,10-epoxy- decanoyl (AEO) 3-(4-aroyl-1 H- propenamide C₁₄H₁₂N₂O₃pyrrol-2-yl)- N-hydroxy-2- propenamide Suberoylanilide hydroxamic acidC₁₄H₂₀N₂O₃ hydroxamic acid m-Carboxycinnamic hydroxamic acid C₁₀H₁₀N₂O₄acid bis- hydroxamide Apicidin¹ cyclopeptide C₂₉H₃₈N₅O₆ Fusarium CHAP1(trichostatin hydroxamic/ spp. A + trapoxin B) porphryin derivatives¹cyclo(N-O-methyl-L-tryptophanyl-L-isoleucinyl-D-pipecolinyl-L-2-amino-8-oxodecanoyl)IV. Methods of Treating Cardiac Hypertrophy

A. Therapeutic Regimens

In one embodiment of the present invention, methods for the treatment ofcardiac hypertrophy utilizing HDAC inhibitors are provided. For thepurposes of the present application, treatment comprises reducing one ormore of the symptoms of cardiac hypertrophy, such as reduced exercisecapacity, reduced blood ejection volume, increased left ventricular enddiastolic pressure, increased pulmonary capillary wedge pressure,reduced cardiac output, cardiac index, increased pulmonary arterypressures, increased left ventricular end systolic and diastolicdimensions, and increased left ventricular wall stress, wall tension andwall thickness-same for right ventricle. In addition, use of HDACinhibitors may prevent cardiac hypertrophy and its associated symptomsfrom arising.

Treatment regimens would vary depending on the clinical situation.However, long term maintenance would appear to be appropriate in mostcircumstances. It also may be desirable treat hypertrophy with HDACinhibitors intermittently, such as within brief window during diseaseprogression. At present, testing indicates that the optimal dosage foran HDAC inhibitor will be the maximal dose before significant toxicityoccurs.

B. Combined Therapy

In another embodiment, it is envisioned to use an HDAC inhibition incombination with other therapeutic modalities. Thus, in addition to thetherapies described above, one may also provide to the patient more“standard” pharmaceutical cardiac therapies. Examples of standardtherapies include, without limitation, so-called “beta blockers,”anti-hypertensives, cardiotonics, anti-thrombotics, vasodilators,hormone antagonists, iontropes, diuretics, endothelin antagonists,calcium channel blockers, phosphodiesterase inhibitors, ACE inhibitors,angiotensin type 2 antagonists and cytokine blockers/inhibitors.

Combinations may be achieved by contacting cardiac cells with a singlecomposition or pharmacological formulation that includes both agents, orby contacting the cell with two distinct compositions or formulations,at the same time, wherein one composition includes the expressionconstruct and the other includes the agent. Alternatively, the HDACinhibitor therapy may precede or follow administration of the otheragent by intervals ranging from minutes to weeks. In embodiments wherethe other agent and expression construct are applied separately to thecell, one would generally ensure that a significant period of time didnot expire between the time of each delivery, such that the agent andexpression construct would still be able to exert an advantageouslycombined effect on the cell. In such instances, it is contemplated thatone would typically contact the cell with both modalities within about12-24 hours of each other and, more preferably, within about 6-12 hoursof each other, with a delay time of only about 12 hours being mostpreferred. In some situations, it may be desirable to extend the timeperiod for treatment significantly, however, where several days (2, 3,4, 5, 6 or 7) to several weeks (1, 2, 3, 4, 5, 6, 7 or 8) lapse betweenthe respective administrations.

It also is conceivable that more than one administration of either anHDAC inhibitor, or the other agent will be desired. In this regard,various combinations may be employed. By way of illustration, where theHDAC inhibitor is “A” and the other agent is “B”, the followingpermutations based on 3 and 4 total administrations are exemplary:

A/B/A B/A/B B/B/A A/A/B B/A/A A/B/B B/B/B/A B/B/A/B A/A/B/B A/B/A/BA/B/B/A B/B/A/A B/A/B/A B/A/A/B B/B/B/A A/A/A/B B/A/A/A A/B/A/A A/A/B/AA/B/B/B B/A/B/B B/B/A/BOther combinations are likewise contemplated.

C. Drug Formulations and Routes for Administration to Patients

Where clinical applications are contemplated, pharmaceuticalcompositions will be prepared in a form appropriate for the intendedapplication. Generally, this will entail preparing compositions that areessentially free of pyrogens, as well as other impurities that could beharmful to humans or animals.

One will generally desire to employ appropriate salts and buffers torender delivery vectors stable and allow for uptake by target cells.Buffers also will be employed when recombinant cells are introduced intoa patient. Aqueous compositions of the present invention comprise aneffective amount of the vector or cells, dissolved or dispersed in apharmaceutically acceptable carrier or aqueous medium. The phrase“pharmaceutically or pharmacologically acceptable” refer to molecularentities and compositions that do not produce adverse, allergic, orother untoward reactions when administered to an animal or a human. Asused herein, “pharmaceutically acceptable carrier” includes solvents,buffers, solutions, dispersion media, coatings, antibacterial andantifingal agents, isotonic and absorption delaying agents and the likeacceptable for use in formulating pharmaceuticals, such aspharmaceuticals suitable for administration to humans. The use of suchmedia and agents for pharmaceutically active substances is well known inthe art. Except insofar as any conventional media or agent isincompatible with the active ingredients of the present invention, itsuse in therapeutic compositions is contemplated. Supplementary activeingredients also can be incorporated into the compositions, providedthey do not inactivate the vectors or cells of the compositions.

The active compositions of the present invention may include classicpharmaceutical preparations. Administration of these compositionsaccording to the present invention may be via any common route so longas the target tissue is available via that route. This includes oral,nasal, or buccal. Alternatively, administration may be by intradermal,subcutaneous, intramuscular, intraperitoneal or intravenous injection.Such compositions would normally be administered as pharmaceuticallyacceptable compositions, as described supra.

The active compounds may also be administered parenterally orintraperitoneally. By way of illustration, solutions of the activecompounds as free base or pharmacologically acceptable salts can beprepared in water suitably mixed with a surfactant, such ashydroxypropylcellulose. Dispersions can also be prepared in glycerol,liquid polyethylene glycols, and mixtures thereof and in oils. Underordinary conditions of storage and use, these preparations generallycontain a preservative to prevent the growth of microorganisms.

The pharmaceutical forms suitable for injectable use include, forexample, sterile aqueous solutions or dispersions and sterile powdersfor the extemporaneous preparation of sterile injectable solutions ordispersions. Generally, these preparations are sterile and fluid to theextent that easy injectability exists. Preparations should be stableunder the conditions of manufacture and storage and should be preservedagainst the contaminating action of microorganisms, such as bacteria andfungi. Appropriate solvents or dispersion media may contain, forexample, water, ethanol, polyol (for example, glycerol, propyleneglycol, and liquid polyethylene glycol, and the like), suitable mixturesthereof, and vegetable oils. The proper fluidity can be maintained, forexample, by the use of a coating, such as lecithin, by the maintenanceof the required particle size in the case of dispersion and by the useof surfactants. The prevention of the action of microorganisms can bebrought about by various antibacterial an antifingal agents, forexample, parabens, chlorobutanol, phenol, sorbic acid, thimerosal, andthe like; In many cases, it will be preferable to include isotonicagents, for example, sugars or sodium chloride. Prolonged absorption ofthe injectable compositions can be brought about by the use in thecompositions of agents delaying absorption, for example, aluminummonostearate and gelatin.

Sterile injectable solutions may be prepared by incorporating the activecompounds in an appropriate amount into a solvent along with any otheringredients (for example as enumerated above) as desired, followed byfiltered sterilization. Generally, dispersions are prepared byincorporating the various sterilized active ingredients into a sterilevehicle which contains the basic dispersion medium and the desired otheringredients, e.g., as enumerated above. In the case of sterile powdersfor the preparation of sterile injectable solutions, the preferredmethods of preparation include vacuum-drying and freeze-dryingtechniques which yield a powder of the active ingredient(s) plus anyadditional desired ingredient from a previously sterile-filteredsolution thereof.

For oral administration the polypeptides of the present inventiongenerally may be incorporated with excipients and used in the form ofnon-ingestible mouthwashes and dentifrices. A mouthwash may be preparedincorporating the active ingredient in the required amount in anappropriate solvent, such as a sodium borate solution (Dobell'sSolution). Alternatively, the active ingredient may be incorporated intoan antiseptic wash containing sodium borate, glycerin and potassiumbicarbonate. The active ingredient may also be dispersed in dentifrices,including: gels, pastes, powders and slurries. The active ingredient maybe added in a therapeutically effective amount to a paste dentifricethat may include water, binders, abrasives, flavoring agents, foamingagents, and humectants.

The compositions of the present invention generally may be formulated ina neutral or salt form. Pharmaceutically-acceptable salts include, forexample, acid addition salts (formed with the free amino groups of theprotein) derived from inorganic acids (e.g., hydrochloric or phosphoricacids, or from organic acids (e.g., acetic, oxalic, tartaric, mandelic,and the like. Salts formed with the free carboxyl groups of the proteincan also be derived from inorganic bases (e.g., sodium, potassium,ammonium, calcium, or ferric hydroxides) or from organic bases (e.g.,isopropylamine, trimethylamine, histidine, procaine and the like.

Upon formulation, solutions are preferably administered in a mannercompatible with the dosage formulation and in such amount as istherapeutically effective. The formulations may easily be administeredin a variety of dosage forms such as injectable solutions, drug releasecapsules and the like. For parenteral administration in an aqueoussolution, for example, the solution generally is suitably buffered andthe liquid diluent first rendered isotonic for example with sufficientsaline or glucose. Such aqueous solutions may be used, for example, forintravenous, intramuscular, subcutaneous and intraperitonealadministration. Preferably, sterile aqueous media are employed as isknown to those of skill in the art, particularly in light of the presentdisclosure. By way of illustration, a single dose may be dissolved in 1ml of isotonic NaCl solution and either added to 1000 ml ofhypodermoclysis fluid or injected at the proposed site of infusion, (seefor example, “Remington's Pharmaceutical Sciences” 15th Edition, pages1035-1038 and 1570-1580). Some variation in dosage will necessarilyoccur depending on the condition of the subject being treated. Theperson responsible for administration will, in any event, determine theappropriate dose for the individual subject. Moreover, for humanadministration, preparations should meet sterility, pyrogenicity,general safety and purity standards as required by FDA Office ofBiologics standards.

V. Screening Methods

The present invention further comprises methods for identifyinginhibitors of HDACs that are useful in the prevention or reversal ofcardiac hypertrophy. These assays may comprise random screening of largelibraries of candidate substances; alternatively, the assays may be usedto focus on particular classes of compounds selected with an eye towardsstructural attributes that are believed to make them more likely toinhibit the function of HDACs.

To identify an HDAC inhibitor, one generally will determine the functionof an HDAC in the presence and absence of the candidate substance. Forexample, a method generally comprises:

-   -   (a) providing a candidate modulator;    -   (b) admixing the candidate modulator with an HDAC;    -   (c) measuring HDAC activity; and    -   (d) comparing the activity in step (c) with the activity in the        absence of the candidate modulator,        wherein a difference between the measured activities indicates        that the candidate modulator is, indeed, a modulator of the        compound, cell or animal.

Assays also may be conducted in isolated cells or in organisms.Typically, HDAC activity is measured by providing a histone with alabeled acetyl group and measuring release of the label from the histonemolecule.

It will, of course, be understood that all the screening methods of thepresent invention are useful in themselves notwithstanding the fact thateffective candidates may not be found. The invention provides methodsfor screening for such candidates, not solely methods of finding them.

1. Modulators

As used herein the term “candidate substance” refers to any moleculethat may potentially inhibit HDAC activity. The candidate substance maybe a protein or fragment thereof, a small molecule, or even a nucleicacid. It may prove to be the case that the most useful pharmacologicalcompounds will be compounds that are structurally related to known HDACinhibitors, listed elsewhere in this document. Using lead compounds tohelp develop improved compounds is known as “rational drug design” andincludes not only comparisons with know inhibitors and activators, butpredictions relating to the structure of target molecules.

The goal of rational drug design is to produce structural analogs ofbiologically active polypeptides or target compounds. By creating suchanalogs, it is possible to fashion drugs, which are more active orstable than the natural molecules, which have different susceptibilityto alteration or which may affect the function of various othermolecules. In one approach, one would generate a three-dimensionalstructure for a target molecule, or a fragment thereof. This could beaccomplished by x-ray crystallography, computer modeling or by acombination of both approaches.

It also is possible to use antibodies to ascertain the structure of atarget compound activator or inhibitor. In principle, this approachyields a pharmacore upon which subsequent drug design can be based. Itis possible to bypass protein crystallography altogether by generatinganti-idiotypic antibodies to a finctional, pharmacologically activeantibody. As a mirror image of a mirror image, the binding site ofanti-idiotype would be expected to be an analog of the original antigen.The anti-idiotype could then be used to identify and isolate peptidesfrom banks of chemically- or biologically-produced peptides. Selectedpeptides would then serve as the pharmacore. Anti-idiotypes may begenerated using the methods described herein for producing antibodies,using an antibody as the antigen.

On the other hand, one may simply acquire, from various commercialsources, small molecular libraries that are believed to meet the basiccriteria for useful drugs in an effort to “brute force” theidentification of useful compounds. Screening of such libraries,including combinatorially-generated libraries (e.g., peptide libraries),is a rapid and efficient way to screen large number of related (andunrelated) compounds for activity. Combinatorial approaches also lendthemselves to rapid evolution of potential drugs by the creation ofsecond, third and fourth generation compounds modeled of active, butotherwise undesirable compounds.

Candidate compounds may include fragments or parts ofnaturally-occurring compounds, or may be found as active combinations ofknown compounds, which are otherwise inactive. It is proposed thatcompounds isolated from natural sources, such as animals, bacteria,fungi, plant sources, including leaves and bark, and marine samples maybe assayed as candidates for the presence of potentially usefulpharmaceutical agents. It will be understood that the pharmaceuticalagents to be screened could also be derived or synthesized from chemicalcompositions or man-made compounds. Thus, it is understood that thecandidate substance identified by the present invention may be peptide,polypeptide, polynucleotide, small molecule inhibitors or any othercompounds that may be designed through rational drug design startingfrom known inhibitors or stimulators.

Other suitable modulators include antisense molecules, ribozymes, andantibodies (including single chain antibodies), each of which would bespecific for the target molecule. Such compounds are described ingreater detail elsewhere in this document. For example, an antisensemolecule that bound to a translational or transcriptional start site, orsplice junctions, would be ideal candidate inhibitors.

In addition to the modulating compounds initially identified, theinventors also contemplate that other sterically similar compounds maybe formulated to mimic the key portions of the structure of themodulators. Such compounds, which may include peptidomimetics of peptidemodulators, may be used in the same manner as the initial modulators.

2. In vitro Assays

A quick, inexpensive and easy assay to run is an in vitro assay. Suchassays generally use isolated molecules, can be run quickly and in largenumbers, thereby increasing the amount of information obtainable in ashort period of time. A variety of vessels may be used to run theassays, including test tubes, plates, dishes and other surfaces such asdipsticks or beads.

A technique for high throughput screening of compounds is described inWO 84/03564. Large numbers of small peptide test compounds aresynthesized on a solid substrate, such as plastic pins or some othersurface. Such peptides could be rapidly screening for their ability tobind and inhibit HDACs.

3. In cyto Assays

The present invention also contemplates the screening of compounds fortheir ability to modulate HDACs in cells. Various cell lines can beutilized for such screening assays, including cells specificallyengineered for this purpose.

4. In vivo Assays

In vivo assays involve the use of various animal models of heartdisease, including transgenic animals, that have been engineered to havespecific defects, or carry markers that can be used to measure theability of a candidate substance to reach and effect different cellswithin the organism. Due to their size, ease of handling, andinformation on their physiology and genetic make-up, mice are apreferred embodiment, especially for transgenics. However, other animalsare suitable as well, including rats, rabbits, hamsters, guinea pigs,gerbils, woodchucks, cats, dogs, sheep, goats, pigs, cows, horses andmonkeys (including chimps, gibbons and baboons). Assays for inhibitorsmay be conducted using an animal model derived from any of thesespecies.

Treatment of animals with test compounds will involve the administrationof the compound, in an appropriate form, to the animal. Administrationwill be by any route that could be utilized for clinical purposes.Determining the effectiveness of a compound in vivo may involve avariety of different criteria, including but not limited to. Also,measuring toxicity and dose response can be performed in animals in amore meaningful fashion than in in vitro or in cyto assays.

VI. Definitions

As used herein, the term “heart failure” is broadly used to mean anycondition that reduces the ability of the heart to pump blood. As aresult, congestion and edema develop in the tissues. Most frequently,heart failure is caused by decreased contractility of the myocardium,resulting from reduced coronary blood flow; however, many other factorsmay result in heart failure, including damage to the heart valves,vitamin deficiency, and primary cardiac muscle disease. Though theprecise physiological mechanisms of heart failure are not entirelyunderstood, heart failure is generally believed to involve disorders inseveral cardiac autonomic properties, including sympathetic,parasympathetic, and baroreceptor responses. The phrase “manifestationsof heart failure” is used broadly to encompass all of the sequelaeassociated with heart failure, such as shortness of breath, pittingedema, an enlarged tender liver, engorged neck veins, pulmonary ratesand the like including laboratory findings associated with heartfailure.

The term “treatment” or grammatical equivalents encompasses theimprovement and/or reversal of the symptoms of heart failure (i.e., theability of the heart to pump blood). “Improvement in the physiologicfunction” of the heart may be assessed using any of the measurementsdescribed herein (e.g., measurement of ejection fraction, fractionalshortening, left ventricular internal dimension, heart rate, etc.), aswell as any effect upon the animal's survival. In use of animal models,the response of treated transgenic animals and untreated transgenicanimals is compared using any of the assays described herein (inaddition, treated and untreated non-transgenic animals may be includedas controls). A compound which causes an improvement in any parameterassociated with heart failure used in the screening methods of theinstant invention may thereby be identified as a therapeutic compound.

The term “dilated cardiomyopathy” refers to a type of heart failurecharacterized by the presence of a symmetrically dilated left ventriclewith poor systolic contractile function and, in addition, frequentlyinvolves the right ventricle.

The term “compound” refers to any chemical entity, pharmaceutical, drug,and the like that can be used to treat or prevent a disease, illness,sickness, or disorder of bodily function. Compounds comprise both knownand potential therapeutic compounds. A compound can be determined to betherapeutic by screening using the screening methods of the presentinvention. A “known therapeutic compound” refers to a therapeuticcompound that has been shown (e.g., through animal trials or priorexperience with administration to humans) to be effective in suchtreatment. In other words, a known therapeutic compound is not limitedto a compound efficacious in the treatment of heart failure.

As used herein, the term “agonist” refers to molecules or compoundswhich mimic the action of a “native” or “natural” compound. Agonists maybe homologous to these natural compounds in respect to conformation,charge or other characteristics. Thus, agonists may be recognized byreceptors expressed on cell surfaces. This recognition may result inphysiologic and/or biochemical changes within the cell, such that thecell reacts to the presence of the agonist in the same manner as if thenatural compound was present. Agonists may include proteins, nucleicacids, carbohydrates, or any other molecules that interact with amolecule, receptor, and/or pathway of interest.

As used herein, the term “cardiac hypertrophy” refers to the process inwhich adult cardiac myocytes respond to stress through hypertrophicgrowth. Such growth is characterized by cell size increases without celldivision, assembling of additional sarcomeres within the cell tomaximize force generation, and an activation of a fetal cardiac geneprogram. Cardiac hypertrophy is often associated with increased risk ofmorbidity and mortality, and thus studies aimed at understanding themolecular mechanisms of cardiac hypertrophy could have a significantimpact on human health.

As used herein, the terms “antagonist” and “inhibitor” refer tomolecules or compounds which inhibit the action of a cellular factorthat may be involved in cardiac hypertrophy. Antagonists may or may notbe homologous to these natural compounds in respect to conformation,charge or other characteristics. Thus, antagonists may be recognized bythe same or different receptors that are recognized by an agonist.Antagonists may have allosteric effects which prevent the action of anagonist. Alternatively, antagonists may prevent the function of theagonist. In contrast to the agonists, antagonistic compounds do notresult in pathologic and/or biochemical changes within the cell suchthat the cell reacts to the presence of the antagonist in the samemanner as if the cellular factor was present. Antagonists and inhibitorsmay include proteins, nucleic acids, carbohydrates, or any othermolecules which bind or interact with a receptor, molecule, and/orpathway of interest.

As used herein, the term “modulate” refers to a change or an alterationin the biological activity. Modulation may be an increase or a decreasein protein activity, a change in binding characteristics, or any otherchange in the biological, finctional, or immunological propertiesassociated with the activity of a protein or other structure ofinterest. The term “modulator” refers to any molecule or compound whichis capable of changing or altering biological activity as describedabove.

The term “β-adrenergic receptor antagonist” refers to a chemicalcompound or entity that is capable of blocking, either partially orcompletely, the beta (β) type of adrenoreceptors (i.e., receptors of theadrenergic system that respond to catecholamines, especiallynorepinephrine). Some β-adrenergic receptor antagonists exhibit a degreeof specificity for one receptor sybtype (generally β₁); such antagonistsare termed “β₁-specific adrenergic receptor antagonists” and“β₂-specific adrenergic receptor antagonists.” The term β-adrenergicreceptor antagonist” refers to chemical compounds that are selective andnon-selective antagonists. Examples of β-adrenergic receptor antagonistsinclude, but are not limited to, acebutolol, atenolol, butoxamine,carteolol, esmolol, labetolol, metoprolol, nadolol, penbutolol,propanolol, and timolol. The use of derivatives of known β-adrenergicreceptor antagonists is encompassed by the methods of the presentinvention. Indeed any compound, which functionally behaves as aβ-adrenergic receptor antagonist is encompassed by the methods of thepresent invention.

The terms “angiotensin-converting enzyme inhibitor” or “ACE inhibitor”refer to a chemical compound or entity that is capable of inhibiting,either partially or completely, the enzyme involved in the conversion ofthe relatively inactive angiotensin I to the active angiotensin II inthe rennin-angiotensin system. In addition, the ACE inhibitorsconcomitantly inhibit the degradation of bradykinin, which likelysignificantly enhances the antihypertensive effect of the ACEinhibitors. Examples of ACE inhibitors include, but are not limited to,benazepril, captopril, enalopril, fosinopril, lisinopril, quiapril andramipril. The use of derivatives of known ACE inhibitors is encompassedby the methods of the present invention. Indeed any compound, whichfunctionally behaves as an ACE inhibitor, is encompassed by the methodsof the present invention.

As used herein, the term “genotypes” refers to the actual geneticmake-up of an organism, while “phenotype” refers to physical traitsdisplayed by an individual. In addition, the “phenotype” is the resultof selective expression of the genome (i.e., it is an expression of thecell history and its response to the extracellular environment). Indeed,the human genome contains an estimated 30,000-35,000 genes. In each celltype, only a small (ie., 10-15%) fraction of these genes are expressed.

VII. EXAMPLES

The following examples are included to further illustrate variousaspects of the invention. It should be appreciated by those of skill inthe art that the techniques disclosed in the examples which followrepresent techniques and/or compositions discovered by the inventor tofunction well in the practice of the invention, and thus can beconsidered to constitute preferred modes for its practice. However,those of skill in the art should, in light of the present disclosure,appreciate that many changes can be made in the specific embodimentswhich are disclosed and still obtain a like or similar result withoutdeparting from the spirit and scope of the invention.

Example 1

Materials and Methods

Cell culture. Ventricular myocytes from one-day-old rats were plated atlow density in MEM with 5% calf serum, and studied in serum-free MEM.Cultures were treated with PE (#P6126, Sigma-Aldrich Corp., St. Louis,Mo.), IL-1 (#501-RL, R&D Systems, Minneapolis, Minn.), TSA (#GR-309,BIOMOL Research Laboratories, Inc., Plymouth Meeting, Pa.) or theirvehicles (ascorbic acid for PE; bovine serum albumin for IL-1; dimethylsulfoxide for TSA).

Detection of acetylated lysine residues. Total cell extract wassubjected to Western blot analysis using antibodies from Cell SignalingTechnology (Beverly, Mass.) (acetylated lysine antibody: #9441,acetylated histone H3 antibody at Lysine 9: #9671, acetylated histone H3antibody at Lysine 23: #9674, histone H3 antibody: #9712). Nuclearlocalization of acetylated histone H3 was examined by inununostainingusing the same antibodies.

Quantification of myocyte hypertrophy and myocyte-specific mRNAexpression. Growth of cultured myocytes was quantified by content ofradiolabeled protein after continuous incubation with ¹⁴C-phenylalanine.For evaluation of the myocyte gene program, total RNA was extracted fromcells with TRIZol (GIBCO, Carlsbad, Calif.) and used in RNase protectionassay with probes for SERCA, α-/β-MyHC, ANP, BNP, and cardiac α-actin.All samples also included glyceraldehyde phosphate dehydrogenase (GAPDH)as an internal control for RNA loading.

Transfection. Myocytes were transfected using calcium-phosphateco-precipitation with cytomegalovirus promoter driven Flag-taggedexpression vectors for HDACs 1, 4, 5 and reporter plasmids carrying therat promoters for SERCA (3500 bp), αMyHC (2900 bp), or βMyHC (3300 bp)driving expression 7 of the chroramphenicol acetyltransferase (CAT)gene. Reporter expression was evaluated after 48 hours as describedpreviously with corection for transfection efficiency with SEAP (BDBiosciences Clontech, Palo Alto, Calif.). Over-expression of HDACs wasconfirmed by Western blot analyses using anti-Flag M2 antibody(Sigma-Aldrich Corp. St. Louis, Mo.).

Results

TSA increases protein acetylation in cardiac myocytes. Initialexperiments were directed at confirming that TSA was able to inhibitHDAC activity in cardiac myocytes, reasoning that this should result inan overall increase in protein acetylation. The degree of acetylationwas determined using antibodies specific for acetylated lysine residues.Inventors showed by both Western blot and cellular immunofluoresenceanalyses that exposure to TSA for 24 hours effectively increasedacetylated lysine residues in a number of proteins and specificallythose in Histone H3.

TSA enhances agonist-induced growth, but reverses hypertrophy associatedgene repression. Although TSA by itself had no effect on myocyte growth,inventors found that it enhanced the individual hypertrophic responsesto both PE and IL-1. Both hypertrophic stimuli down-regulated SERCA(FIG. 1A) and αMyHC (FIG. 1B) expression and the combined exposure toboth agonists resulted in further repression. In contrast, TSA increasedthe basal expression of both SERCA2a and αMyHC mRNAs. TSA pre-treatmentalso resulted in a substantial reversal in the repression of SERCAexpression by both hypertrophic stimuli. Notably, although TSA resultedin a nearly complete reversal of the PE effect on αMyHC expression, thiseffect was less prominent in the case of IL-1 treated (or co-treated)cells. Inventors previously showed that co-treatment of cardiac myocyteswith both PE and IL-1 suppressed the usual PE induction of αMyHCexpression by nearly 50%. It is intriguing that although TSA had noeffects on either the basal expression or PE-induction of this gene, itincreased αMyHC expression in the presence of IL-1 alone and reversedthe IL-1 effect in PE/IL-1 co-treated cells. A similar reversal was alsoseen with the sACT gene (Wang and Long, unpublished data). Notably, TSAdid not affect gene expression of cardiac α-actin, ANP, or BNP under anyhypertrophic treatment condition (data not shown).

Over-expression of HDAC repressed promoter activities ofmyocyte-specific genes. In agreement with the studies of mRNA expressionfor these target genes, TSA also increased the basal promoter activitiesof both SERCA2 (FIG. 2A) and αMyHC (FIG. 2B) genes but not that of βMyHC(FIG. 2C). Further, co-transfection of these constructs with expressionvectors for HDACs1 or 4 also decreased promoter activities for bothSERCA (FIG. 2A) and αMyHC (FIG. 2D) genes. In contrast, however, HDAC5failed to inhibit the promoter activities of either gene despite levelsof expression similar to that of the other isoforms (data not shown).Notably, all three HDAC constructs were able to attenuate the PE-inducedincrease in αMyHC promoter activity (FIG. 2D).

Example 2

Materials and Methods

Cardiomyocyte isolation. Hearts were harvested from 15-daytimed-pregnant female Sprague-Dawley rats (Harlan, Houston, Tex.). Aftermincing in phosphate-buffered saline, cardiomyocytes were isolated fromsuccessive digestion fractions of 0.1% (w/v) Pancreatin (Sigma, St.Louis, Mo.) solution. Fractions were collected; resuspended in platingmedium, pooled; and then plated for 2 hours to separate fibroblasts fromcardiomyocyte population. Suspended cells were recollected and plated in6-well dishes at 1×10⁶ cells/well for transfection andimmunofluorescence experiments, and 2×10⁶ cells in 10 cm dishes for RNAanalysis.

Transcription assay. Twenty-four hours after plating, cells weretransfected with total of 1 μg/ml for 5 hrs using Lipofectamine Plusreagent (Invitrogen, Carlsbad, Calif.). Transfected cells were incubated24 hrs then treated for an additional 24 hrs. Cells were lysed and theirlysates assayed with the Luciferase Assay System (Promega, Madison,Wis.) for luminescence using Lucysoft 2 luminometer (Rosys Anthos, NewCastle, Del.).

Chemilumenescence. Neonatal cardiomyocytes were seeded onto 96-wellplates and treated for 72 hrs. The cells were washed twice in 1×PBS,fixed in 4% paraformaldehyde/1×PBS, and permeabilized with 0.1%Triton-X100. After blocking, the cells were incubated 1 hr. with 10μg/ml monoclonal anti-ANF antibody (Biodesign). The wells were washedtwice with 1% BSA/1×PBS and then incubated for 1 hr. with goatanti-mouse IgG-Fc-HRP (Jackson Labs, location) at 1:1000 in 1×PBS/1%BSA. Cells were washed twice with 1% BSA/1×PBS, twice with 1×PBS, thenblotted dry. Luminol (Pierce, Rockford, Ill.) was added and thechemiluminescence was detected in a Fusion Plate Reader (PerkinElmer/Packard).

Dot Blot analysis. Total RNA was isolated from cardiomyocytes that wereeither untreated, treated with phenylephrine, treated with TSA, orco-treated with phenylephrine and TSA. One microgram of RNA was blottedonto Nitrocellulose (Bio-Rad, Hercules, Calif.) and hybridized at 50° C.for 14 hrs with end-labeled oligos. (ANF,5′-aatgtgaccaagctgcgtgacacaccacaagggcttaggatcttttgcgatctgctcaag-3, SEQID NO 1; αSKactin5′-tggagcaaaacagaatggctggctttaatgcttcaagttttccatttcctttccacaggg-3′,SEQ ID NO2; αMyHC,5′cgaacgtttatgtttattgtggattggccacagcgagggtctgctggagagg-3′, SEQ ID NO 3;βMyHC5′-gctttat tctgcttccacctaaagggctgttgcaaa ggctccaggtctgagggcttc-3′,SEQ ID NO 4; GAPDH5′-ggaacatgtagaccatgtag ttgaggtcaatgaag-3′, SEQ ID NO5). The blots were washed twice in 2×SSC/0.5% SDS solution and exposedto film (Kodak, Rochester, N.Y.) or phosphoimager (Amersham Bioscience,Sunnyvale, Calif.). The intensity of the hybridization of the probes wasmeasured using ImageQuant© (Amersham Bioscience, Sunnyvale, Calif.).

Immunostaining. Glass coverslips were coated with laminin (Invitrogen,Carlsbad, Calif.) by solublizing laminin in 1×PBS (40 μg/ml), by dippingthe coverslips in the solution and by allowing them to air-dry. Cellswere treated for 24 hrs, washed, fixed 10 min. with 3.7% formaldehyde,washed with 1×PBS and permeabolized with 1×PBS containing 3% BSA and0.1% NP-40 (Sigma, St. Louis, Mo.). Primary Antibodies were in 1×PBScontaining 3% BSA and 0.1% NP-40 for 30 min, then washed three times in1×PBS. The secondary FITC or TRITC antibodies (Vector Laboratories,Inc., Burlingame, Calif.) were incubated (1:200) in same buffer solutionas the primary antibodies, then washed in 1×PBS, covered andsubsequently visualized. Images were captured using a digital camera(Hamamatsu Photonics, Hamamatsu City, Japan).

Protein synthesis. Cardiomyocytes were incubated with (1.0 μCi/ml; 172Ci/mmol sp. activity) tritiated-leucine (ICN Biochemicals, Inc., Irvine,Calif.) in treated RPMI media (Invitrogen, Carlsbad, Calif.). After 6hrs incubation, the cells were washed twice with 1×PBS, then incubatedin 10% TCA on ice for 30 min. Afterwards, the cells were washed twicewith 5% TCA, once with water, and then lysed in 0.25 NaOH. Lysates weremeasured in one-sixth volume of scintillation fluid by a scintillationcounter (Beckman, Fullerton, Calif.).

S6 Ribosomal protocol. After blocking, cells were incubated in 1%BSA/1×PBS containing 50 μg/ml anti-S6 protein (Cell Signaling, location)for 1 hr. After washing, the cells were incubated with IgG-HRP (JacksonLabs, location) at a 1:400 dilution. The cells were then washed twice in1% BSA/1×PBS, in 1×PBS, then blotted dry. Luminol (Pierce, Rockford,Ill.) was added and the chemiluminescence was detected in a Fusionreader (Perkin-Elmer/Packard).

Gene chip and analysis. RNA was isolated using Trizol (Invitrogen,Carlsbad, Calif.) from untreated, phenylephrine-treated, TSA-treated,and phenylephine/TSA co-treated rat neonatal cardiomyocytes. The RNAswere prepared and hybridized on U34A chips (Affymetrix, Inc., SantaClara, Calif.) according to Affymetrix protocols. The intensity ofhybridization was detected by and changes in gene expression weredetermined and analyzed by Micro Array Suite 5.0 (Affymetrix, Inc.,Santa Clara, Calif.).

Results

Because histone deacetylases (HDACs) regulate gene expression, theinventors analyzed whether HDAC inhibition would alter the expression ofgenes associated with cardiac hypertrophy. Atrial natriuretic factor(ANF) is one such gene, and its expression increases in presence of thehypertrophic agonists. In order to determine whether HDAC inhibitionaffects ANF gene activation, transfection experiments were performedwith the ANF promoter and transfected cardiomyocytes were treated withphenylephrine and several HDAC inhibitors. Treatment of cardiomyocyteswith trichostatin (TSA), sodium butyrate (NaBut) or HC-toxin (HC) didnot activate the ANF promoter. The HDAC inhibitors, however, did blockthe promoter's activation by phenylephrine treatment completely (FIG.3A). This effect was specific, because cardiomyocytes treated eitherwith each HDAC inhibitor alone or together with phenylephrine increasedthe transcriptional activity of the CMV-Lac Z reporter (FIG. 3B),indicating that the action of these pharmacological agents was specificto the transcriptional control of ANF and not from generaltranscriptional inhibition.

Inventors then examined whether increasing doses of TSA and sodiumbutyrate were cytotoxic to cultured cardiomyocytes. To determine cellmortality, the release of adenylate kinase from cardiomyocytes into theculture medium was assayed. This assay is a known measurement for theintegrity of the cell membrane: membranes become permeable in dyingcells causing the cells release adenylate kinase. Increasing doses ofTSA (up to 100 nM) and sodium butyrate (up to 25 nM) did little toincrease adenylate kinase in the culture medium, indicating an absenceof increased cell death by TSA and sodium butyrate (FIGS. 3C & 3D). Inthe single time-point experiments, 85 nM TSA or 5 mM sodium butyratewere used, so these results indicate that inactivation of ANFtranscription is a direct effect of HDAC inhibition and not an indirectconsequence of cytotoxicity by the HDAC inhibitors.

To determine whether endogenous gene expression paralleled thetransfection results, the inventors looked at endogenous RNA levels ofANF from cardiomyocytes under the various treatment conditions. RNA dotblot analysis of phenylephrine-treated cardiomyocytes showed anapproximate three-fold increase in the expression of ANF in response tophenylephrine treatment; however, co-treatment of phenylephrine-treatedcells with the different HDAC inhibitors (TSA, NaBut or HC-toxin)prevented the phenylephrine-induced ANF response (FIG. 4A), in agreementwith the transfection results previously mentioned.

Prior data has shown that a low dose of TSA can induce the ANFexpression by acetylation of the ANF locus and by inactivation of thetranscription repressor, NRSE. To address whether there is adose-dependent effect of HDAC inhibitors, inventors examined ANFexpression after treating primary cardiomyocytes with increasingconcentrations of TSA (FIG. 4B) and sodium butyrate (FIG. 4C) in theabsence and presence of the hypertrophic stimulants serum (FBS),phenylephrine (PE) or endothelin-1 (ET-1). At very low doses (0.2 nM) ofsodium butyrate (FIG. 4C), inventors observed a near two-fold increasein ANF expression. There was only a marginal increase increase with TSA(FIG. 4B). However, the HDAC inhibitors at all other concentrations didnot induce ANF production, and with increasing concentrations, theycountered the induction of ANF expression normally observed aftertreating cultured cardiomyocytes with the growth stimulants FBS, PE andET-1 (FIGS. 4B and C). The minimal concentrations that inhibited thehypertrophic response of each growth stimulant were 40 nM TSA and 5 mMsodium butyrate, which mimicked the three-to-four-fold reduction of ANFin transcription observed in the transfection and dot blot experiments.These doses were well below the threshold of cytotoxicity.

Cardiac hypertrophy is associated with the reprogramming of fetal genesin addition to ANF. The inventors wished to determine whether othermembers of the fetal gene cascade were affected by treatment of TSA.Quantitative analysis of the fold change of α-sk expression and βMyHC,in addition to ANF, showed that HDAC inhibition resulted in thesuppression of other genes activated by the hypertrophic stimulant,phenylephrine (FIGS. 5A and B). Furthermore, in addition todown-regulating the fetal myosin chain isoform (βMyHC) isoform, TSAtreatment of cardiac myocytes induced the expression of αMyHC, the adultmyosin heavy chain isoform normally reduced in hypertrophiccardiomyocytes (FIG. 5B). These data taken together indicate that HDACinhibition suppresses the transcriptional reprogramming of the genecascade associated with cardiomyocyte hypertrophy.

Staining for ANF protein showed that cardiomyocytes treated withphenylephrine or serum induced a perinuclear accumulation of ANF proteincompared to unstimulated cells (data not shown). Cardiomyocytes treatedwith TSA lacked accumulation of ANF protein and the addition of TSA tocardiomyocytes treated either with phenylephrine or with serumdramatically reduced ANF protein accumulation. Immunocytochemicalstaining for α-actinin showed that HDAC inhibition antagonized thereorganization of the sarcomere, another phenomenon associated withcardiomyocyte hypertrophy. Unstimulated cardiomyocytes maintained anamorphous shape with no apparent structural organization of thesarcomere (α-actinin). Hypertrophic agonists phenylephrine, serum, andET-1 potently stimulated the organization of the sarcomere as part of ahighly ordered cytoskeletal structure. Interestingly, TSA did affectcardiomyocyte morphology. Although TSA-treated cells did not changesize, they tended to acquire a “starred” appearance by growing narrowextensions from the main body of the cell. However, they lackedorganization of the sarcomere. The effect of TSA treatment was moredramatic in the presence of growth stimulants, because it affected thehypertrophic morphology normally induced by phenylephrine, serum orET-1. TSA-treated cardiomyocytes lacked fully organized sarcomeres.

The inventors then determined whether TSA antagonized the increase inprotein synthesis normally associated with the hypertrophic response byassaying for changes in protein synthesis and measuring the accumulationof the protein content of the ribosomal subunit, S6. Phenylephrineboosted protein synthesis in the cardiac myocytes by two-fold after 6hours of stimulation; however, co-culturing phenylephrine with the HDACinhibitors TSA and sodium butyrate had little effect on the stimulationof protein synthesis normally induced with phenylephrine (FIG. 6). Yet,by 24 hrs after co-treatment, HDAC inhibitors antagonized the proteinsynthesis normally induced by PE or serum in a dose-dependent manner(FIG. 6). This suggests that the prevention of the organization of thesarcomere by HDAC inhibition is an effect specific to transcriptionregulation.

Previous work has shown that TSA treatment of yeast results in a changein gene expression in only a subset of genes. If this is true forcardiomyocytes, then it is possible that a limited number of genes areresponsible for the suppression of the hypertrophic phenotype. Toidentify these genes, inventors assayed the expression of approximatelyeight-thousand genes by gene chip array. Subsequent graphic analysis ofthe assays of the expression between the gene changes in thephenylephrine- and phenylephrine/TSA-treated cells revealed that themajority of genes clustered linearly. The majority of transcriptsremained relatively unchanged (less than a three-fold change in geneexpression) between the chip hybridized with RNA fromphenylephrine-treated cells and the chip hybridized with RNA fromphenylephrine/TSA-treated cells. This suggests that the relative numberof genes responsible for the suppression of phenylephrine-inducedcardiomyocyte growth by TSA treatment is low.

From the reduced number of genes whose expression levels were altered byphenylephrine, TSA or their combination, inventors identified sevengenes that had a consistent two-or-more-fold difference betweenphenylephrine treatment and the TSA-treated groups: phenylephrine/TSAand TSA. Three genes were up-regulated by phenylephrine treatment anddown-regulated by TSA: cytochrome oxidase subunit VIII, mouse T-complexprotein and insulin growth factor binding protein-3 (FIG. 7A). Fourgenes down-regulated by phenylephrine and up-regulated by TSA were bigTau-microtubule-associated protein, ubiquitin carboxyl-terminalhydrolase, Thy-1 cell-surface glycoprotein and MyHC class I antigen(FIG. 7B). Northern analysis confirmed the expression results of thegene chip array (data not shown).

All of the compositions and methods disclosed and claimed herein can bemade and executed without undue experimentation in light of the presentdisclosure. While the compositions and methods of this invention havebeen described in terms of preferred embodiments, it will be apparent tothose of skill in the art that variations may be applied to thecompositions and methods, and in the steps or in the sequence of stepsof the methods described herein without departing from the concept,spirit and scope of the invention. More specifically, it will beapparent that certain agents which are both chemically andphysiologically related may be substituted for the agents describedherein while the same or similar results would be achieved. All suchsimilar substitutes and modifications apparent to those skilled in theart are deemed to be within the spirit, scope and concept of theinvention as defined by the appended claims.

XI. References

The following references, to the extent that they provide exemplaryprocedural or other details supplementary to those set forth herein, arespecifically incorporated herein by reference:

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1. A method of treating heart failure comprising: (a) identifying apatient having heart failure; and (b) administering to said patient ahistone deacetylase inhibitor.
 2. The method of claim 1, wherein saidhistone deacetylase inhibitor is selected from the group consisting oftrichostatin A, trapoxin B, MS 275-27, m-carboxycinnamic acidbis-hydroxamide, depudecin, oxamfiatin, apicidin, suberoylanilidehydroxamic acid, Scriptaid, pyroxamide,2-amino-8-oxo-9,10-epoxy-decanoyl,3-(4-aroyl-1H-pyrrol-2-yl)-N-hydroxy-2-propenamide and FR901228.
 3. Themethod of claim 1, wherein administering comprises intravenousadministration of said histone deacetylase inhibitor.
 4. The method ofclaim 1, wherein administering comprises oral, transdermal, sustainedrelease, suppository, or sublingual administration.
 5. The method ofclaim 1, further comprising administering to said patient a secondtherapeutic regimen.
 6. The method of claim 5 wherein said secondtherapeutic regimen is selected from the group consisting of a betablocker, an iontrope, diuretic, ACE-I, AII antagonist, and Ca⁺⁺-blocker.7. The method of claim 5, wherein said second therapeutic regimen isadministered at the same time as said histone deacetylase inhibitor. 8.The method of claim 5, wherein said second therapeutic regimen isadministered either before or after said histone deacetylase inhibitor.9. The method of claim 1, wherein treating comprises improving one ormore symptoms of heart failure.
 10. The method of claim 9, wherein saidone or more symptoms comprises increased exercise capacity, increasedblood ejection volume, left ventricular end diastolic pressure,pulmonary capillary wedge pressure, cardiac output, cardiac index,pulmonary artery pressures, left ventricular end systolic and diastolicdimensions, left and right ventricular wall stress, or wall tension,quality of life, disease-related morbidity and mortality.